TimiRGeN

DOI: 10.18129/B9.bioc.TimiRGeN    

This is the development version of TimiRGeN; for the stable release version, see TimiRGeN.

Time sensitive microRNA-mRNA integration, analysis and network generation tool

Bioconductor version: Development (3.16)

TimiRGeN (Time Incorporated miR-mRNA Generation of Networks) is a novel R package which functionally analyses and integrates time course miRNA-mRNA differential expression data. This tool can generate small networks within R or export results into cytoscape or pathvisio for more detailed network construction and hypothesis generation. This tool is created for researchers that wish to dive deep into time series multi-omic datasets. TimiRGeN goes further than many other tools in terms of data reduction. Here, potentially hundreds-of-thousands of potential miRNA-mRNA interactions can be whittled down into a handful of high confidence miRNA-mRNA interactions affecting a signalling pathway, across a time course.

Author: Krutik Patel [aut, cre]

Maintainer: Krutik Patel <krutik.patel at newcastle.ac.uk>

Citation (from within R, enter citation("TimiRGeN")):

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("TimiRGeN")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews Clustering, Network, Pathways, Software, TimeCourse, Visualization, miRNA
Version 1.7.0
In Bioconductor since BioC 3.12 (R-4.0) (1.5 years)
License GPL-3
Depends R (>= 4.1), Mfuzz, MultiAssayExperiment
Imports biomaRt, clusterProfiler, dplyr (>= 0.8.4), FreqProf, gtools (>= 3.8.1), gplots, ggdendro, gghighlight, ggplot2, graphics, grDevices, igraph (>= 1.2.4.2), RCy3, readxl, reshape2, rWikiPathways, scales, stats, tidyr (>= 1.0.2), stringr (>= 1.4.0)
LinkingTo
Suggests BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db, org.Mm.eg.db, testthat, rmarkdown
SystemRequirements
Enhances
URL https://github.com/Krutik6/TimiRGeN/
BugReports https://github.com/Krutik6/TimiRGeN/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary TimiRGeN_1.7.0.zip (64-bit only)
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/TimiRGeN
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TimiRGeN
Package Short Url https://bioconductor.org/packages/TimiRGeN/
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